The electrochemical nitrate reduction reaction (NO3RR) to ammonia offers a promising approach for wastewater treatment and ammonia synthesis. However, the generation of various by-products, such as nitrite ions (NO2-), and the occurrence of the competitive hydrogen evolution reaction (HER) complicate reaction pathways, causing unwanted electrical energy consumption and reducing the product selectivity. Herein, we introduce a pulse electrolysis approach to control the sequential accumulation and conversion of NO2- intermediates during the NO3RR using a conductive rod-like zinc-based metal organic framework (Zn-MOF) electrode with precise atomic structures. This strategy substantially improves both the yield and Faraday efficiency (FENH3) of NH3 production relative to constant-potential electrolysis. After a long-term stability test, the high-purity ammonia product in the electrolyte was successfully extracted via an argon (Ar) stripping process, showing a practical way to turn wastewater nitrate into valuable ammonia-derived products. This study presents a promising strategy for rationally designing metal organic framework (MOFs) electro-catalysts with precise atomic structures and controlling complex reactions, thereby minimizing side reactions, significantly boosting nitrate-to-ammonia conversion efficiency.